Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.00128/0.00128, allocations: 77.55 kB / 19.76 MB, free: 2.027 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.001425/0.001425, allocations: 156.2 kB / 23.01 MB, free: 4.949 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 1.349/1.349, allocations: 177.2 MB / 203.4 MB, free: 8.961 MB / 190.1 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo): time 0.1227/0.1227, allocations: 17.44 MB / 277.2 MB, free: 15.19 MB / 270.1 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis") [Timeout 660]
"Notification: Chemical requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.001967/0.001967, allocations: 63.91 kB / 412.6 MB, free: 5.566 MB / 382.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09832/0.1003, allocations: 59.88 MB / 472.5 MB, free: 9.566 MB / 446.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/Obsolete.mo:14335:7-14335:66:writable] Warning: An inner declaration for outer component system could not be found and was automatically generated.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/Obsolete.mo:14335:7-14335:66:writable] Notification: The diagnostics message for the missing inner is: 
Your model is using an outer \"system\" component but
an inner \"system\" component is not defined.
For simulation drag Modelica.Fluid.System into your model
to specify system properties.
Notification: Performance of NFInst.instantiate(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis): time 0.4095/0.5098, allocations: 26.17 MB / 498.6 MB, free: 38.99 MB / 446.1 MB
Notification: Performance of NFInst.instExpressions: time 0.01242/0.5222, allocations: 14.71 MB / 0.5013 GB, free: 31.12 MB / 446.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0006353/0.5228, allocations: 20.41 kB / 0.5013 GB, free: 31.11 MB / 446.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0007537/0.5236, allocations: 310.4 kB / 0.5016 GB, free: 30.95 MB / 446.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.003051/0.5267, allocations: 1.468 MB / 0.5031 GB, free: 30.08 MB / 446.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004084/0.5307, allocations: 2.021 MB / 0.505 GB, free: 28.9 MB / 446.1 MB
Notification: Performance of NFFlatten.flatten: time 0.001288/0.532, allocations: 1.549 MB / 0.5066 GB, free: 28.14 MB / 446.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006089/0.5326, allocations: 0.6835 MB / 0.5072 GB, free: 27.82 MB / 446.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0006702/0.5333, allocations: 0.7808 MB / 0.508 GB, free: 27.54 MB / 446.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0009242/0.5342, allocations: 0.7798 MB / 0.5087 GB, free: 27.28 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002061/0.5344, allocations: 139.1 kB / 0.5089 GB, free: 27.28 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.003775/0.5382, allocations: 1.701 MB / 0.5105 GB, free: 26.9 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002395/0.5384, allocations: 323.4 kB / 0.5108 GB, free: 26.71 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0005344/0.539, allocations: 0.5842 MB / 0.5114 GB, free: 26.41 MB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.00474/0.5437, allocations: 3.439 MB / 0.5148 GB, free: 24.96 MB / 446.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.409e-06/0.5437, allocations: 3.938 kB / 0.5148 GB, free: 24.95 MB / 446.1 MB
Notification: Performance of FrontEnd: time 1.803e-06/0.5437, allocations: 0 / 0.5148 GB, free: 24.95 MB / 446.1 MB
Notification: Performance of Transformations before backend: time 1.561e-05/0.5437, allocations: 0 / 0.5148 GB, free: 24.95 MB / 446.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 276
 * Number of variables: 276
Notification: Performance of Generate backend data structure: time 0.002736/0.5465, allocations: 1.77 MB / 0.5165 GB, free: 23.9 MB / 446.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.353e-05/0.5465, allocations: 8.281 kB / 0.5165 GB, free: 23.9 MB / 446.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001063/0.5476, allocations: 274.9 kB / 0.5168 GB, free: 23.81 MB / 446.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0009055/0.5485, allocations: 0.6214 MB / 0.5174 GB, free: 23.43 MB / 446.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001053/0.5486, allocations: 135.6 kB / 0.5175 GB, free: 23.32 MB / 446.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000162/0.5488, allocations: 113.6 kB / 0.5176 GB, free: 23.29 MB / 446.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001769/0.5505, allocations: 1.338 MB / 0.5189 GB, free: 22.73 MB / 446.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.415e-05/0.5505, allocations: 5.219 kB / 0.5189 GB, free: 22.73 MB / 446.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001044/0.5506, allocations: 41.34 kB / 0.519 GB, free: 22.7 MB / 446.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.351e-05/0.5507, allocations: 26.38 kB / 0.519 GB, free: 22.7 MB / 446.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002221/0.5529, allocations: 1.676 MB / 0.5206 GB, free: 22.2 MB / 446.1 MB
Warning: The model contains alias variables with redundant start and/or conflicting nominal values. It is recommended to resolve the conflicts, because otherwise the system could be hard to solve. To print the conflicting alias sets and the chosen candidates please use -d=aliasConflicts.
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.005148/0.558, allocations: 3.385 MB / 0.5239 GB, free: 20.31 MB / 446.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002831/0.5609, allocations: 1.876 MB / 0.5258 GB, free: 19.71 MB / 446.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000692/0.5616, allocations: 0.5307 MB / 0.5263 GB, free: 19.5 MB / 446.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.00477/0.5663, allocations: 2.79 MB / 0.529 GB, free: 18.31 MB / 446.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.765e-05/0.5664, allocations: 46.62 kB / 0.5291 GB, free: 18.26 MB / 446.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.364e-06/0.5664, allocations: 0 / 0.5291 GB, free: 18.26 MB / 446.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01283/0.5792, allocations: 3.416 MB / 0.5324 GB, free: 16.92 MB / 446.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.675e-05/0.5792, allocations: 62.84 kB / 0.5325 GB, free: 16.86 MB / 446.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004848/0.5797, allocations: 0.5717 MB / 0.533 GB, free: 16.58 MB / 446.1 MB
Notification: Performance of collectPreVariables (initialization): time 5.204e-05/0.5798, allocations: 41.42 kB / 0.5331 GB, free: 16.54 MB / 446.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002053/0.58, allocations: 0.558 MB / 0.5336 GB, free: 16.08 MB / 446.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001775/0.5801, allocations: 347 kB / 0.5339 GB, free: 15.81 MB / 446.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002472/0.5804, allocations: 235.6 kB / 0.5342 GB, free: 15.69 MB / 446.1 MB
Notification: Performance of setup shared object (initialization): time 8.519e-05/0.5805, allocations: 390.6 kB / 0.5345 GB, free: 15.34 MB / 446.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005037/0.581, allocations: 363.2 kB / 0.5349 GB, free: 15.21 MB / 446.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0006719/0.5816, allocations: 0.744 MB / 0.5356 GB, free: 14.59 MB / 446.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001309/0.583, allocations: 1.2 MB / 0.5368 GB, free: 13.68 MB / 446.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.534e-06/0.583, allocations: 7.969 kB / 0.5368 GB, free: 13.68 MB / 446.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003541/0.5865, allocations: 1.475 MB / 0.5382 GB, free: 12.56 MB / 446.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.1e-05/0.5865, allocations: 12.8 kB / 0.5382 GB, free: 12.55 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.335e-05/0.5865, allocations: 12 kB / 0.5382 GB, free: 12.54 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001837/0.5884, allocations: 244.5 kB / 0.5385 GB, free: 12.36 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00131/0.5897, allocations: 328.4 kB / 0.5388 GB, free: 12.08 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.004198/0.5939, allocations: 3.579 MB / 0.5423 GB, free: 8.461 MB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000842/0.5947, allocations: 45.81 kB / 0.5423 GB, free: 8.418 MB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001/0.5948, allocations: 67.94 kB / 0.5424 GB, free: 8.355 MB / 446.1 MB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 58
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (152):
 * Single equations (assignments): 150
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of prepare postOptimizeDAE: time 0.0003635/0.5952, allocations: 277.3 kB / 0.5427 GB, free: 8.078 MB / 446.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000146/0.5953, allocations: 92.19 kB / 0.5427 GB, free: 7.988 MB / 446.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003613/0.5989, allocations: 1.325 MB / 0.544 GB, free: 6.855 MB / 446.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.623e-06/0.599, allocations: 12 kB / 0.5441 GB, free: 6.844 MB / 446.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.928e-06/0.599, allocations: 0 / 0.5441 GB, free: 6.844 MB / 446.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.356e-05/0.599, allocations: 5.438 kB / 0.5441 GB, free: 6.844 MB / 446.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001049/0.6, allocations: 0.803 MB / 0.5448 GB, free: 6.086 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.559e-06/0.6, allocations: 4 kB / 0.5448 GB, free: 6.082 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001128/0.6011, allocations: 218.5 kB / 0.5451 GB, free: 5.898 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.00178/0.6029, allocations: 232.6 kB / 0.5453 GB, free: 5.73 MB / 446.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.043e-05/0.603, allocations: 27.75 kB / 0.5453 GB, free: 5.707 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.003856/0.6069, allocations: 3.493 MB / 0.5487 GB, free: 2.16 MB / 446.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.465e-06/0.6069, allocations: 4.031 kB / 0.5487 GB, free: 2.156 MB / 446.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.003783/0.6107, allocations: 1.727 MB / 0.5504 GB, free: 0.5781 MB / 446.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002531/0.6109, allocations: 77.56 kB / 0.5505 GB, free: 0.5039 MB / 446.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001/0.611, allocations: 24.61 kB / 0.5505 GB, free: 492 kB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0004853/0.6115, allocations: 21.2 kB / 0.5505 GB, free: 472 kB / 446.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001999/0.6117, allocations: 83.67 kB / 0.5506 GB, free: 428 kB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.546e-05/0.6118, allocations: 40.03 kB / 0.5506 GB, free: 392 kB / 446.1 MB
Notification: Performance of sorting global known variables: time 0.000365/0.6121, allocations: 369.5 kB / 0.551 GB, free: 80 kB / 446.1 MB
Notification: Performance of sort global known variables: time 7e-08/0.6121, allocations: 0 / 0.551 GB, free: 80 kB / 446.1 MB
Notification: Performance of remove unused functions: time 0.002401/0.6145, allocations: 0.6812 MB / 0.5517 GB, free: 15.41 MB / 462.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 5
 * Number of states: 5 (solution.temperature,CH4.logn,CO2.logn,H2O.logn,H2.logn)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (98):
 * Single equations (assignments): 96
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of Backend phase and start with SimCode phase: time 0.001606/0.6161, allocations: 0.8268 MB / 0.5525 GB, free: 14.66 MB / 462.1 MB
Notification: Performance of simCode: created initialization part: time 0.00241/0.6185, allocations: 1.193 MB / 0.5536 GB, free: 13.55 MB / 462.1 MB
Notification: Performance of simCode: created event and clocks part: time 4.177e-06/0.6186, allocations: 256 / 0.5536 GB, free: 13.55 MB / 462.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001174/0.6197, allocations: 0.7018 MB / 0.5543 GB, free: 12.88 MB / 462.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.00108/0.6208, allocations: 204.8 kB / 0.5545 GB, free: 12.71 MB / 462.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003468/0.6243, allocations: 1.999 MB / 0.5565 GB, free: 10.81 MB / 462.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004599/0.6247, allocations: 449.7 kB / 0.5569 GB, free: 10.46 MB / 462.1 MB
Notification: Performance of simCode: alias equations: time 0.0007894/0.6255, allocations: 223.6 kB / 0.5571 GB, free: 10.27 MB / 462.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003368/0.6259, allocations: 162.6 kB / 0.5573 GB, free: 10.14 MB / 462.1 MB
Notification: Performance of SimCode: time 6.21e-07/0.6259, allocations: 4 kB / 0.5573 GB, free: 10.13 MB / 462.1 MB
Notification: Performance of Templates: time 0.03912/0.665, allocations: 23.92 MB / 0.5806 GB, free: 4.254 MB / 478.1 MB
"
[Timeout remaining time 659]
make -j1 -f Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile [Timeout 660]
(rm -f Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis  -abortSlowSimulation -alarm=480 -s ida -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 5.588677427964285]
Failed to read output from testmodel.py, exit status != 0:
0.6735369040397927 0.6880194709999999 0.141277449
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7fd22bc2afe0>